Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 629

5 diseases · 10 shared-gene connections
5 Diseases
2 Unique genes
0.433 Avg. similarity score
Deafness, autosomal dominant, 78 Most-connected disease (4 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Deafness, autosomal dominant, 78 4 4 1
Delpire-mcneill syndrome 4 4 1
Intestinal malrotation 4 4 1
Kilquist syndrome 4 4 1
Lymphatic system disease 4 4 2

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
SLC12A2 5 / 5 Deafness, autosomal dominant, 78, Delpire-mcneill syndrome, Intestinal malrotation, Kilquist syndrome and 1 more
What do these columns mean?
Connections in cluster
How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners
How many of those links are statistically significant (FDR q < 0.05).
Curated genes
Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes)
How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y)
x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count
Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment
Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value
Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster)
Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster)
Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Cation-coupled Chloride cotransporters
SLC12A2
 Reactome 1 / 7 858× 1.17e-3 1.27e-2 ✓ sig.
Vibrio cholerae infection
SLC12A2
 KEGG 1 / 51 118× 8.48e-3 5.13e-2
Adherens junction
PTPRM
 KEGG 1 / 93 64.6× 1.54e-2 7.39e-2
Salivary secretion
SLC12A2
 KEGG 1 / 93 64.6× 1.54e-2 7.39e-2
Pancreatic secretion
SLC12A2
 KEGG 1 / 102 58.9× 1.69e-2 7.79e-2
Cell adhesion molecules
PTPRM
 KEGG 1 / 160 37.5× 2.65e-2 1.01e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
positive regulation of cell volume
SLC12A2
 GO:0045795 1 / 1 9,344× 1.07e-4 3.25e-3 ✓ sig.
positive regulation of aspartate secretion
SLC12A2
 GO:1904450 1 / 2 4,672× 2.14e-4 5.31e-3 ✓ sig.
inorganic cation import across plasma membrane
SLC12A2
 GO:0098659 1 / 2 4,672× 2.14e-4 5.31e-3 ✓ sig.
inorganic anion import across plasma membrane
SLC12A2
 GO:0098658 1 / 2 4,672× 2.14e-4 5.31e-3 ✓ sig.
regulation of matrix metallopeptidase secretion
SLC12A2
 GO:1904464 1 / 2 4,672× 2.14e-4 5.31e-3 ✓ sig.
regulation of spontaneous synaptic transmission
SLC12A2
 GO:0150003 1 / 4 2,336× 4.28e-4 8.53e-3 ✓ sig.
transepithelial ammonium transport
SLC12A2
 GO:0070634 1 / 4 2,336× 4.28e-4 8.53e-3 ✓ sig.
negative regulation of D-glucose transmembrane transport
PTPRM
 GO:0010829 1 / 7 1,335× 7.49e-4 1.23e-2 ✓ sig.
positive regulation of D-glucose transmembrane transport
PTPRM
 GO:0010828 1 / 8 1,168× 8.56e-4 1.33e-2 ✓ sig.
hyperosmotic response
SLC12A2
 GO:0006972 1 / 8 1,168× 8.56e-4 1.33e-2 ✓ sig.
negative regulation of vascular wound healing
SLC12A2
 GO:0061044 1 / 8 1,168× 8.56e-4 1.33e-2 ✓ sig.
transepithelial chloride transport
SLC12A2
 GO:0030321 1 / 9 1,038× 9.63e-4 1.42e-2 ✓ sig.
intracellular chloride ion homeostasis
SLC12A2
 GO:0030644 1 / 10 934× 1.07e-3 1.51e-2 ✓ sig.
ammonium transmembrane transport
SLC12A2
 GO:0072488 1 / 11 849× 1.18e-3 1.59e-2 ✓ sig.
chloride ion homeostasis
SLC12A2
 GO:0055064 1 / 13 719× 1.39e-3 1.75e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deafness, autosomal dominant, 78 Delpire-mcneill syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal dominant, 78 Intestinal malrotation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal dominant, 78 Kilquist syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Delpire-mcneill syndrome Intestinal malrotation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Delpire-mcneill syndrome Kilquist syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal malrotation Kilquist syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal dominant, 78 Lymphatic system disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Delpire-mcneill syndrome Lymphatic system disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intestinal malrotation Lymphatic system disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Kilquist syndrome Lymphatic system disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.